We're probably decades away from Shor's algorithm. Right now we're mostly dealing in the realm of "Noisy Intermediate-Scale Quantum" machines (NISQ). The abstract of this paper gives a good summary of where we're at: https://arxiv.org/abs/1801.00862

The "operating system" has little to do with accelerating that (outside of maybe cutting out some development cost + time), though in theory they can provide some algorithms and optimizations that minimize noise and decoherence.